As an aside, I find it annoying that some bundles don't include all the games; for example Splinter Cell's bundle is missing Pandora Tormorrow and The Hitman bundle is missing Contracts. Obviously contractual disputes since neither game is on Steam at all but these couldn't have been worked out by now? These aren't exactly new games...

I don't think new copies of Pandora Tomorrow or Contracts can legally be sold anywhere anymore, physical or digital. You can still find old physical copies online, though.